We previously showed using microarray profiling biotechnology that stepwise transformation and metastatic progression of SCC in a murine model results in the expression of gene programs related to the signal transcription factor NF-kappaB. Inhibition of NF-kappaB modulated over half the up or down-regulated genes differentially expressed, and attenuated the malignant phenotype, indicating it may be a critical target for prevention or therapy of head and neck cancer. Gene expression profiling and bioinformatic analysis of the promoters of gene clusters differentially expressed in human HNSCC provided evidence for increased prevalence of binding motifs for NF-kappaB as well as other signal transcription factors, such as p53, AP-1, STAT3 and EGR-1 (Yan et al, Genome Biology, 2007, 2008). NF-kappaB, p53, AP-1, STAT3 and EGR-1 activation has previously been associated with pathogenesis and therapeutic resistance, and the subsets expressing wt or mt 53 have been reported to differ in response to chemotherapy. These observations suggested the hypothesis that key alterations in a network of signal transcription factors can interact in determining gene expression and development of HNSCC of differing malignant potential and sensitivity or resistance to therapy. One relationship recently identified was between NF-kB member c-REL and p53 members p53, p63 and p73. This led to demonstration that cytokine TNF induced cREL interacts with p63, displacing p73 from growth arrest and apoptotic genes and the nucleus of HNSCC (Lu et al, Cancer Res, 2011). Novel p63, cREL as well as classical p53 and NF-kB sites were defined in a broader set of cancer genes and validated by ChIP assay (Yang et al, Cancer Res, 2011). An analysis of ChIP sequencing of global gene expression regulated by cREL, p63 and p73 in HNSCC has revealed the importance of these interactions genome-wide (Lu and Si et al, manuscript submitted). Next generation RNA and DNA sequencing of HNSCC has been undertaken to identify important genetic and microRNA drivers that regulate broader changes in gene expression and malignant phenotype. We have contributed to identification of significantly decreased microRNAs and upregulated target RNAs from data from 279 HNSCC tumors as part of The Cancer Genome Atlas (TCGA) head and neck cancer group (TCGA, Nature, 2015). Preliminary studies in HNSCC cell lines confirm important roles for 3 of these genes, and 2 candidate therapeutics demonstrating in vitro and in vivo activity in preclinical models. We have identified a candidate family of miRNAs whose decrease contributes to the increased expression of genes in HNSCC. We have completed comprehensive RNA, microRNA and exome sequencing of a large panel of HNSCC cell lines, to identify key mutations, and alterations in copy number, mRNA and miRNA that define models refective of tumor subsets for functional and therapeutic analysis. We developed NF-kB reporter lines and our proposal was selected for a functional genomics screen to identify important genes and candidate targets for prevention/therapy. We have completed a comprehensive genomic and proteomic analysis and comparison of 1409 head and neck, lung, esophageal, cervical, and bladder squamous cell carcinomas. These studies identify common and distinguishing molecular features of these cancers.